PeptideAtlasapplication/xmlftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_5286_searchdatabase_tandem.fastaftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_Search_Results_5286_201109020925.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_mzXML_201109020920.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_Search_Results_5286_201109020925.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_mzXML_201109020920.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_prot_5286_201109020927.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_5286_tandem.paramsftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_prot_5286_201109020927.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Mtuberculosis/PAe001767/PAe001767_READMEprimaryOK200Akhilesh Pandey and colleagues at the Institute of Bioinformatics, Bangalore, India.TPP'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=3027'pandey@jhmi.eduPeptideAtlasProteomicsLTQ Orbitrap VelosMycobacterium TuberculosisThe genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ~250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes.Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.Kelkar Dhanashree S DS, Kumar Dhirendra D, Kumar Praveen P, Balakrishnan Lavanya L, Muthusamy Babylakshmi B, Yadav Amit Kumar AK, Shrivastava Priyanka P, Marimuthu Arivusudar A, Anand Sridhar S, Sundaram Hema H, Kingsbury Reena R, Harsha H C HC, Nair Bipin B, Prasad T S Keshava TS, Chauhan Devendra Singh DS, Katoch Kiran K, Katoch Vishwa Mohan VM, Kumar Prahlad P, Chaerkady Raghothama R, Ramachandran Srinivasan S, Dash Debasis D, Pandey Akhilesh AMass Spectrum Analysis, Bacillus tuberculosis, Spectroscopy, Mass Spectrum, Bacterium tuberculosis, MS, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), determination, Analyses, Mycobacterium tuberculosis var. hominis, chemical analysis, Mycobacterium tuberculosis H37Rv, Mass, Mass., Spectrometry, assay, Analysis, Spectrum Analyses, Mass Spectrum Analyses, Spectrum Analysis, Mass Spectroscopy, Mycobacterium tuberculosis typus humanusKoch's Disease, Infection, Koch Disease, Tuberculosis, Mycobacterium tuberculosis, Mycobacterium tuberculosis Infection, Tuberculoses, Republic of India., Mycobacterium tuberculosis Infections, Infections, Kochs Disease, active tuberculosisLUZP5, T2SS-associated complexes, hCAP-G2., Sec-dependent secretion system-associated complex, mCAP-G2, CAP-G2, 5830426I05Rik, general secretion pathway-associated complex, Luzp5, main terminal branch, CAPG2, MTB, MtbIPP2A2, Materials, determination, protein, Progress Reports, composed of, Long Term, Mendosicutes, 5730420M11Rik, peptide, Polypeptides, peptido, Summary Report, Mycobacterium tuberculosis var. hominis, Tuberculosis, Analysis, protein aggregate, Effect, Summary Reports, WMS, Koch's Disease, Mass Spectrum Analysis, Bacillus tuberculosis, Bacterium tuberculosis, Koch Disease, SET, peptides, Genomes, Metabacteria, Analyses, Progress Report, TAF-I, composition, ecotype, Bacteria Woese et al. 2024, DmelCG4299, Progress, IGAAD, set, Field Reports, DmelCG10574, Prokaryotae, Strains, Procaryotae, GPHYSD2, Long-Term Effects, SGS, phapii, Archaebacteria, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), Genome Sequencing, Longterm Effect, StF-IT-1, Spectrum Analysis, predicted, ACMICD, Spectroscopy, Complete Genome, count, Investigative Report, Genetic Materials, prokaryotes, cultivar, END, Genetic Material, parent ion, HLA-DR-associated protein II, DI-2, MS/MS, content, I-2Dm, Field, Spectrometry, INSDC_feature:gene, whole genome, MASS, CG4299, I-2PP1, Report, TAF-IBETA, precursor ion, Material, Cistron, TAF-Ibeta, Polypeptide, Mycobacterium tuberculosis Infection, Genetic Material., Strains and Sprains, i2pp2a, active tuberculosis, Prokaryota, Effects, number, FBN, Gene, Coding, eubacteria, Spectrum Analyses, precursor, protein-containing complex, PHAPII, Protein Gm1141, Investigative, ECTOL1, Core Genome, Mass, Gene Products, Bacteriobiota, Sprains, Medical, Mass Spectroscopy, Complete, Whole Genome, Genetic, Clinical, Infections, Longterm, MS2, Medical Coding, ipp2a2, Accessory Genome, Complete Genome Sequencing, 2pp2a, Long-Term, Mycobacterium tuberculosis Infections, Monera, Sequencing, CG10574, OCTD, Bacteria (ex Cavalier-Smith 1987), 2PP2A, taf-ibeta, Whole, dSET, dSet, peptidos, Mycobacterium tuberculosis, Long-Term Effect, species, Archaebiota, Investigative Reports, HHT1, bacteria, Edg, Kochs Disease, protein complex, Sprain, Proteins, Novel protein, igaad, compositionality, Cistrons, Pangenome, Peptide, group, strain, polypeptide, MS, native protein, I-2PP2A, chemical analysis, Protein, Research Reports, Dm I-2, Long Term Effects, Strain, I2PP2A, Infection, MFS1, Tuberculoses, Mass Spectrum Analyses, tandem MS, Data Base, WMS2, Mass Spectrum, ensemble, not Bacteria Haeckel 1894, Mycobacterium tuberculosis H37Rv, archaea, Longterm Effects, Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, Pan-genome, Reports, prokaryote, cardinality, structure, SSKS, Peptid, assay, ORW1, Summary, AA407739, Field Report, Mycobacterium tuberculosis typus humanusfalseMtb_H37Rv_IOBM. tuberculosis H37Rv from Akhilesh Pandey and colleagues at the Institute of Bioinformatics, Bangalore, India.2011-12-312016-03-29PAe00176721969609